Re: [Freesurfer] Recon-all -hires

Hi Bruce,

I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)".

Cheers, Hweeling

On 21 November 2017 at 23:57, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

oh, this may be a version mismatch then. Which version of FS are you using?

On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

Dear Bruce,

...

Thanks for your reply. I checked the folder and did not find the file that was requested.

What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.lta'.

Cheers, Hweeling

On Nov 21, 2017 18:05, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote: Hi Hweeling

  what is FREESURFER_HOME set to in the environment? Does that file

exist? It is a standard part of our distribution

  cheers
  Bruce


   On Tue, 21 Nov 2017, Hwee Ling Lee wrote:

        Dear all,

        I have T1 images collected from the 7T MRI scanner.

        I downloaded the most recent freesurfer software, and

followed all instructions to install the software before using it.

        I would like to segment the T1 data using its high resolution

image, and also to segment the hippocampal subfields.

        For command, I use this:

        recon-all -all -s <subject name> -hires -i <subject dicom T1

image frame 1 location>

        However, I get an error message:

        cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca

        I'm not sure what I did wrong.

        Also, how can I combine high resolution segmentation and

hippocampal subfields segmentation?

        Could someone please help?

        Thanks.

        Best regards,
        Hweeling





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